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SVS7 Manual

Installing and Initializing
- Installation Overview
- Release Notes
Understanding the Interface and Workflow
- General Genetic Association Analysis Workflow
- Interface Overview
- Navigating the Welcome Screen
- Project Navigator
Importing Your Data Into A Project
- Importing Data
- Text File
- Third Party File
- PED/TPED/BED File
- Golden Helix DSF File
- Legacy Golden Helix GHD File
- Affymetrix Files
- Illumina DSF File
- Agilent Files
- NimbleGen Data Summary Files
- Importing PBAT Family-Based Data
- Import Scripts
Genetic Marker Maps and Affymetrix Library Files
- Genetic Marker Maps Overview
- Convert Text File into Marker Map DSM Format
- Download Affymetrix Annotation Files
- Managing the MarkerMaps Folder
- Applying a Genetic Marker Map to a Spreadsheet
- Exporting an Applied Genetic Marker Map to a DSM file
- Downloading Affymetrix Library (CDF) Files
Spreadsheets
- Spreadsheet Overview
- Working with a Single Spreadsheet
- Editing a Spreadsheet
- Working with Multiple Spreadsheets
Scripting and Other Integrated Statistical Tools
- Integrated Tools Overview
- The Python Shell Window
- The Python Editor Window
- Running Scripts
- Obtaining Add-On Scripts
- Scripting Reference
Data Quality Assessment
- Quality Control Overview
- Genotype Statistics by Marker
- Genotype Filtering by Marker
- Genotype Statistics by Sample
- PBAT Family-Based QC Statistics
- Principal Component Analysis Overview
- Genotypic Principal Component Analysis
- Numeric Principal Component Analysis
- Correcting for Stratification by Genomic Control
Analysis
- Genotype Association Tests
- Haplotype Association Tests
- Haplotype Block Detection
- Runs of Homozygosity
- Numeric Association Tests
- Regression Analysis
PBAT Family-Based Analysis
- PBAT Family-Based Analysis Overview
- Using PBAT Capabilities Through SVS
- Pre-Study Power Calculation
- PBAT Genotype Analysis
- PBAT CNV Analysis
Copy Number Analysis
- Copy Number Analysis Overview
- Preparing Log2 Ratio Data
- Using CNAM Optimal Segmenting
- Outputs from CNAM Optimal Segmenting
- CNV Association Tests
- Visualizing Copy Number Analysis Results
Visualizing Data
- Types of Plots Available
- Plot Viewer
- Genome Browser
- Opening the Plot Viewer
- Using the Graph Control Interface
- Using the Data Console
- Docking, Un-docking or Hiding Plot Viewer Subwindows
- Zooming in the Graph View
- Using LD Plots
- Haplotype Tables
- Heat Maps
- Creating Specialized Plots
- Genome Maps
Export Options for Data and Plots
- Exporting Spreadsheet Data
- Saving or Printing Graphs
Formulas and Theories: The Science Behind SNP and Variation Suite
- General Statistics
- Permutation Testing Methodology
- Linear Regression
- Logistic Regression
- Haplotype Frequency Estimation Methods
- Formulas for Principal Component Analysis
- Runs Of Homozygosity (ROH) Algorithm
- Quantile Normalization of Affymetrix CEL Files
- CNAM Optimal Segmentation Algorithm
Appendices
EULA
Installing the Third-Party Condor ® Package
- Installing Condor ® Overview
- Downloading and Using the Installation Wizard
- Troubleshooting Techniques and Common Issues
Extracting Affymetrix Copy Number Data for use in SVS
- Extracting Affymetrix Copy Number Data Overview
- Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool
- Creating CNCHP Files Using Affymetrix Genotyping Console 2.0
- Affymetrix CNT File Format
Exporting Data from GenomeStudio
- Exporting Data From GenomeStudio Overview
- Exporting Genotype Data using the Final Report
- Exporting Data using the SVS DSF Export 4.0 Plug-In
Platform Notes
- Microsoft Windows
A Glossary of Terms Used in Genetic Analysis
References

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6 Scripting and Other Integrated Statistical Tools

6.1 Integrated Tools Overview
6.2 The Python Shell Window
6.3 The Python Editor Window
6.4 Running Scripts
6.5 Obtaining Add-On Scripts
6.6 Scripting Reference

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